Multiple sequence alignment - TraesCS1D01G362000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G362000 chr1D 100.000 3646 0 0 1 3646 444385001 444381356 0.000000e+00 6734
1 TraesCS1D01G362000 chr1D 98.765 324 1 2 3326 3646 325494078 325494401 1.140000e-159 573
2 TraesCS1D01G362000 chr1A 96.725 1893 47 4 85 1974 540065207 540063327 0.000000e+00 3138
3 TraesCS1D01G362000 chr1A 97.449 1333 34 0 2006 3338 540063334 540062002 0.000000e+00 2274
4 TraesCS1D01G362000 chr1B 96.102 1719 63 4 1 1716 604564925 604563208 0.000000e+00 2800
5 TraesCS1D01G362000 chr1B 95.943 1627 59 5 1718 3338 604563147 604561522 0.000000e+00 2632
6 TraesCS1D01G362000 chr1B 87.393 698 58 10 2505 3200 604645361 604644692 0.000000e+00 774
7 TraesCS1D01G362000 chr5D 100.000 308 0 0 3339 3646 376040292 376040599 1.470000e-158 569
8 TraesCS1D01G362000 chr6D 99.677 310 1 0 3337 3646 172894269 172894578 5.280000e-158 568
9 TraesCS1D01G362000 chr6D 99.676 309 1 0 3338 3646 104461470 104461778 1.900000e-157 566
10 TraesCS1D01G362000 chr2D 99.357 311 2 0 3336 3646 415064109 415064419 6.830000e-157 564
11 TraesCS1D01G362000 chr7D 97.248 327 7 2 3322 3646 219746893 219747219 1.480000e-153 553
12 TraesCS1D01G362000 chr7D 99.026 308 3 0 3339 3646 219782250 219781943 1.480000e-153 553
13 TraesCS1D01G362000 chr7D 97.538 325 5 2 3322 3646 317117496 317117175 1.480000e-153 553
14 TraesCS1D01G362000 chr3D 96.429 336 8 4 3312 3646 506591541 506591209 5.320000e-153 551
15 TraesCS1D01G362000 chr7A 75.165 757 151 30 1938 2687 88176408 88175682 4.540000e-84 322


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G362000 chr1D 444381356 444385001 3645 True 6734 6734 100.0000 1 3646 1 chr1D.!!$R1 3645
1 TraesCS1D01G362000 chr1A 540062002 540065207 3205 True 2706 3138 97.0870 85 3338 2 chr1A.!!$R1 3253
2 TraesCS1D01G362000 chr1B 604561522 604564925 3403 True 2716 2800 96.0225 1 3338 2 chr1B.!!$R2 3337
3 TraesCS1D01G362000 chr1B 604644692 604645361 669 True 774 774 87.3930 2505 3200 1 chr1B.!!$R1 695
4 TraesCS1D01G362000 chr7A 88175682 88176408 726 True 322 322 75.1650 1938 2687 1 chr7A.!!$R1 749

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
781 785 0.944386 AACTTCACATGTGTCGGTGC 59.056 50.0 24.63 0.0 35.04 5.01 F
1394 1399 2.015227 GAGAGGAGGAGGAAGCAGCG 62.015 65.0 0.00 0.0 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2500 1.207329 AGACCGGTAGAACCAAGCATC 59.793 52.381 7.34 0.0 38.47 3.91 R
3353 3464 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.0 0.00 6.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 9.817809 TCATAGTTTTACTGAATAGTGACCATC 57.182 33.333 0.00 0.00 37.78 3.51
175 176 7.566658 AATTATTTGGAGAGAGATAGAGGGG 57.433 40.000 0.00 0.00 0.00 4.79
295 297 2.384828 AGTTGGTTTCAAAGGACCCAC 58.615 47.619 0.00 0.00 34.99 4.61
459 461 6.556146 TTGCAAATACGTACACAACAAAAC 57.444 33.333 0.00 0.00 0.00 2.43
475 477 2.730183 AAACGTCGTTGACATGTGTG 57.270 45.000 12.12 0.00 32.09 3.82
555 557 4.161377 TCTTGTGTGCTATACCTATGTGCA 59.839 41.667 0.00 0.00 0.00 4.57
561 563 1.618837 CTATACCTATGTGCAGGCGGT 59.381 52.381 0.00 0.00 39.53 5.68
612 614 4.321824 CGATGAGAGGAGCACATATGTCAT 60.322 45.833 5.07 3.78 0.00 3.06
641 644 0.964700 CACAGGTGTCTGCTCTCTGA 59.035 55.000 0.00 0.00 44.59 3.27
673 676 5.316167 AGATTTATCAACACTCAACAGGCA 58.684 37.500 0.00 0.00 0.00 4.75
692 695 3.005554 GCATGCATGTGTTGTCTCTAGT 58.994 45.455 26.79 0.00 0.00 2.57
742 746 5.286082 CGCCAAACCGAAAAATCTCAAATAG 59.714 40.000 0.00 0.00 0.00 1.73
781 785 0.944386 AACTTCACATGTGTCGGTGC 59.056 50.000 24.63 0.00 35.04 5.01
1245 1249 2.224523 GGAGAGACATGTTGTTGGTGGA 60.225 50.000 0.00 0.00 0.00 4.02
1394 1399 2.015227 GAGAGGAGGAGGAAGCAGCG 62.015 65.000 0.00 0.00 0.00 5.18
1442 1447 2.509131 TGGTCATGCATTGGAGGATACA 59.491 45.455 0.00 0.00 41.41 2.29
1451 1456 4.686944 GCATTGGAGGATACAAGGATCACA 60.687 45.833 0.00 0.00 41.41 3.58
1531 1536 8.438676 AACAATATTACTAGTGATCAACCAGC 57.561 34.615 5.39 0.00 0.00 4.85
1862 1926 5.917462 GCATTACTTGCCCCTATTCAAAAT 58.083 37.500 0.00 0.00 46.15 1.82
2072 2176 4.138487 AGTCGGGATATTTTGTGTCTCC 57.862 45.455 0.00 0.00 0.00 3.71
2145 2249 5.468746 TGCATTCCACAACTTAGTCTAACAC 59.531 40.000 0.00 0.00 0.00 3.32
2236 2340 5.120674 GGAAAAACATATCCAAGCACTTTGC 59.879 40.000 0.00 0.00 38.48 3.68
2396 2500 1.115467 ATAGTTCTGGTCCCTCGCAG 58.885 55.000 0.00 0.00 0.00 5.18
2450 2554 3.551496 CTTCGGGTTGCAGGCTCCA 62.551 63.158 7.94 0.00 0.00 3.86
2451 2555 3.551496 TTCGGGTTGCAGGCTCCAG 62.551 63.158 7.94 4.78 0.00 3.86
3016 3122 7.925483 CCCAATGACAAAACACAAGAATCTTTA 59.075 33.333 0.00 0.00 0.00 1.85
3156 3263 3.071312 TCATGCATGTTGGCTTTTCCTTT 59.929 39.130 25.43 0.00 35.26 3.11
3288 3398 3.262915 GCCTGCTCCTCATTGTATATCCT 59.737 47.826 0.00 0.00 0.00 3.24
3338 3449 3.509575 GTCTGATAGCGGAGAATGGAGAT 59.490 47.826 0.00 0.00 0.00 2.75
3339 3450 3.509184 TCTGATAGCGGAGAATGGAGATG 59.491 47.826 0.00 0.00 0.00 2.90
3340 3451 3.234353 TGATAGCGGAGAATGGAGATGT 58.766 45.455 0.00 0.00 0.00 3.06
3341 3452 4.407365 TGATAGCGGAGAATGGAGATGTA 58.593 43.478 0.00 0.00 0.00 2.29
3342 3453 4.832823 TGATAGCGGAGAATGGAGATGTAA 59.167 41.667 0.00 0.00 0.00 2.41
3343 3454 3.460857 AGCGGAGAATGGAGATGTAAC 57.539 47.619 0.00 0.00 0.00 2.50
3344 3455 2.128035 GCGGAGAATGGAGATGTAACG 58.872 52.381 0.00 0.00 0.00 3.18
3345 3456 2.128035 CGGAGAATGGAGATGTAACGC 58.872 52.381 0.00 0.00 0.00 4.84
3346 3457 2.484889 GGAGAATGGAGATGTAACGCC 58.515 52.381 0.00 0.00 0.00 5.68
3347 3458 2.484889 GAGAATGGAGATGTAACGCCC 58.515 52.381 0.00 0.00 0.00 6.13
3348 3459 1.837439 AGAATGGAGATGTAACGCCCA 59.163 47.619 0.00 0.00 0.00 5.36
3349 3460 1.940613 GAATGGAGATGTAACGCCCAC 59.059 52.381 0.00 0.00 0.00 4.61
3351 3462 1.252215 TGGAGATGTAACGCCCACGA 61.252 55.000 0.00 0.00 43.93 4.35
3352 3463 0.104304 GGAGATGTAACGCCCACGAT 59.896 55.000 0.00 0.00 43.93 3.73
3353 3464 1.209128 GAGATGTAACGCCCACGATG 58.791 55.000 0.00 0.00 43.93 3.84
3354 3465 0.810031 AGATGTAACGCCCACGATGC 60.810 55.000 0.00 0.00 43.93 3.91
3361 3472 2.342279 GCCCACGATGCGGCTATA 59.658 61.111 0.00 0.00 42.21 1.31
3362 3473 1.079127 GCCCACGATGCGGCTATAT 60.079 57.895 0.00 0.00 42.21 0.86
3363 3474 1.084370 GCCCACGATGCGGCTATATC 61.084 60.000 0.00 0.00 42.21 1.63
3364 3475 0.532573 CCCACGATGCGGCTATATCT 59.467 55.000 0.00 0.00 0.00 1.98
3365 3476 1.469940 CCCACGATGCGGCTATATCTC 60.470 57.143 0.00 0.00 0.00 2.75
3366 3477 1.469940 CCACGATGCGGCTATATCTCC 60.470 57.143 0.00 0.00 0.00 3.71
3367 3478 0.818296 ACGATGCGGCTATATCTCCC 59.182 55.000 0.00 0.00 0.00 4.30
3368 3479 0.817654 CGATGCGGCTATATCTCCCA 59.182 55.000 0.00 0.00 0.00 4.37
3369 3480 1.469940 CGATGCGGCTATATCTCCCAC 60.470 57.143 0.00 0.00 0.00 4.61
3370 3481 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
3371 3482 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
3372 3483 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
3373 3484 0.959553 CGGCTATATCTCCCACGTGT 59.040 55.000 15.65 0.00 0.00 4.49
3374 3485 1.068472 CGGCTATATCTCCCACGTGTC 60.068 57.143 15.65 0.00 0.00 3.67
3375 3486 1.068472 GGCTATATCTCCCACGTGTCG 60.068 57.143 15.65 4.04 0.00 4.35
3376 3487 1.878088 GCTATATCTCCCACGTGTCGA 59.122 52.381 15.65 8.55 0.00 4.20
3377 3488 2.095668 GCTATATCTCCCACGTGTCGAG 60.096 54.545 15.65 17.66 0.00 4.04
3378 3489 1.319541 ATATCTCCCACGTGTCGAGG 58.680 55.000 22.62 14.20 37.35 4.63
3379 3490 1.381928 TATCTCCCACGTGTCGAGGC 61.382 60.000 22.62 0.00 36.35 4.70
3380 3491 3.680786 CTCCCACGTGTCGAGGCA 61.681 66.667 15.65 0.00 36.35 4.75
3381 3492 3.916392 CTCCCACGTGTCGAGGCAC 62.916 68.421 15.65 0.00 36.35 5.01
3391 3502 2.478989 TCGAGGCACGACTTAGAGG 58.521 57.895 2.07 0.00 46.45 3.69
3392 3503 1.226717 CGAGGCACGACTTAGAGGC 60.227 63.158 0.00 0.00 45.77 4.70
3393 3504 1.890894 GAGGCACGACTTAGAGGCA 59.109 57.895 0.00 0.00 0.00 4.75
3394 3505 0.461961 GAGGCACGACTTAGAGGCAT 59.538 55.000 0.00 0.00 0.00 4.40
3395 3506 1.681793 GAGGCACGACTTAGAGGCATA 59.318 52.381 0.00 0.00 0.00 3.14
3396 3507 2.100916 GAGGCACGACTTAGAGGCATAA 59.899 50.000 0.00 0.00 0.00 1.90
3397 3508 2.159085 AGGCACGACTTAGAGGCATAAC 60.159 50.000 0.00 0.00 0.00 1.89
3398 3509 2.202566 GCACGACTTAGAGGCATAACC 58.797 52.381 0.00 0.00 39.61 2.85
3399 3510 2.460918 CACGACTTAGAGGCATAACCG 58.539 52.381 0.00 0.00 46.52 4.44
3400 3511 1.202382 ACGACTTAGAGGCATAACCGC 60.202 52.381 0.00 0.00 46.52 5.68
3401 3512 1.202371 CGACTTAGAGGCATAACCGCA 60.202 52.381 0.00 0.00 46.52 5.69
3402 3513 2.545952 CGACTTAGAGGCATAACCGCAT 60.546 50.000 0.00 0.00 46.52 4.73
3403 3514 3.305131 CGACTTAGAGGCATAACCGCATA 60.305 47.826 0.00 0.00 46.52 3.14
3404 3515 4.238514 GACTTAGAGGCATAACCGCATAG 58.761 47.826 0.00 0.00 46.52 2.23
3405 3516 3.641906 ACTTAGAGGCATAACCGCATAGT 59.358 43.478 0.00 0.00 46.52 2.12
3406 3517 2.533266 AGAGGCATAACCGCATAGTG 57.467 50.000 0.00 0.00 46.52 2.74
3407 3518 1.070758 AGAGGCATAACCGCATAGTGG 59.929 52.381 0.00 0.00 46.52 4.00
3415 3526 1.153353 ACCGCATAGTGGTTTTGTCG 58.847 50.000 0.00 0.00 44.78 4.35
3416 3527 0.179200 CCGCATAGTGGTTTTGTCGC 60.179 55.000 0.00 0.00 0.00 5.19
3417 3528 0.515127 CGCATAGTGGTTTTGTCGCA 59.485 50.000 0.00 0.00 0.00 5.10
3418 3529 1.069568 CGCATAGTGGTTTTGTCGCAA 60.070 47.619 0.00 0.00 0.00 4.85
3419 3530 2.584791 GCATAGTGGTTTTGTCGCAAG 58.415 47.619 0.00 0.00 0.00 4.01
3433 3544 2.099141 CGCAAGAAGGGTCATCTTCA 57.901 50.000 7.26 0.00 44.01 3.02
3434 3545 1.734465 CGCAAGAAGGGTCATCTTCAC 59.266 52.381 7.26 0.00 44.01 3.18
3435 3546 2.783135 GCAAGAAGGGTCATCTTCACA 58.217 47.619 7.26 0.00 44.01 3.58
3436 3547 2.485814 GCAAGAAGGGTCATCTTCACAC 59.514 50.000 7.26 0.00 44.01 3.82
3437 3548 3.743521 CAAGAAGGGTCATCTTCACACA 58.256 45.455 7.26 0.00 44.01 3.72
3438 3549 4.136796 CAAGAAGGGTCATCTTCACACAA 58.863 43.478 7.26 0.00 44.01 3.33
3439 3550 4.647564 AGAAGGGTCATCTTCACACAAT 57.352 40.909 7.26 0.00 44.01 2.71
3440 3551 4.583871 AGAAGGGTCATCTTCACACAATC 58.416 43.478 7.26 0.00 44.01 2.67
3441 3552 3.356529 AGGGTCATCTTCACACAATCC 57.643 47.619 0.00 0.00 0.00 3.01
3442 3553 2.025887 AGGGTCATCTTCACACAATCCC 60.026 50.000 0.00 0.00 0.00 3.85
3443 3554 2.290896 GGGTCATCTTCACACAATCCCA 60.291 50.000 0.00 0.00 33.33 4.37
3444 3555 3.624777 GGTCATCTTCACACAATCCCAT 58.375 45.455 0.00 0.00 0.00 4.00
3445 3556 3.379372 GGTCATCTTCACACAATCCCATG 59.621 47.826 0.00 0.00 0.00 3.66
3446 3557 4.012374 GTCATCTTCACACAATCCCATGT 58.988 43.478 0.00 0.00 0.00 3.21
3447 3558 5.185454 GTCATCTTCACACAATCCCATGTA 58.815 41.667 0.00 0.00 30.84 2.29
3448 3559 5.647658 GTCATCTTCACACAATCCCATGTAA 59.352 40.000 0.00 0.00 30.84 2.41
3449 3560 6.319658 GTCATCTTCACACAATCCCATGTAAT 59.680 38.462 0.00 0.00 30.84 1.89
3450 3561 6.319405 TCATCTTCACACAATCCCATGTAATG 59.681 38.462 0.00 0.00 46.21 1.90
3469 3580 9.699410 ATGTAATGAACAAGAATGGGATAAAGA 57.301 29.630 0.00 0.00 42.70 2.52
3470 3581 9.177608 TGTAATGAACAAGAATGGGATAAAGAG 57.822 33.333 0.00 0.00 34.29 2.85
3471 3582 9.178758 GTAATGAACAAGAATGGGATAAAGAGT 57.821 33.333 0.00 0.00 0.00 3.24
3472 3583 8.655935 AATGAACAAGAATGGGATAAAGAGTT 57.344 30.769 0.00 0.00 0.00 3.01
3473 3584 7.452880 TGAACAAGAATGGGATAAAGAGTTG 57.547 36.000 0.00 0.00 0.00 3.16
3474 3585 6.434028 TGAACAAGAATGGGATAAAGAGTTGG 59.566 38.462 0.00 0.00 0.00 3.77
3475 3586 4.706962 ACAAGAATGGGATAAAGAGTTGGC 59.293 41.667 0.00 0.00 0.00 4.52
3476 3587 4.870021 AGAATGGGATAAAGAGTTGGCT 57.130 40.909 0.00 0.00 0.00 4.75
3477 3588 5.198602 AGAATGGGATAAAGAGTTGGCTT 57.801 39.130 0.00 0.00 0.00 4.35
3478 3589 6.327386 AGAATGGGATAAAGAGTTGGCTTA 57.673 37.500 0.00 0.00 0.00 3.09
3479 3590 6.122964 AGAATGGGATAAAGAGTTGGCTTAC 58.877 40.000 0.00 0.00 0.00 2.34
3480 3591 4.919774 TGGGATAAAGAGTTGGCTTACA 57.080 40.909 0.00 0.00 0.00 2.41
3481 3592 5.249780 TGGGATAAAGAGTTGGCTTACAA 57.750 39.130 0.00 0.00 36.54 2.41
3482 3593 5.826643 TGGGATAAAGAGTTGGCTTACAAT 58.173 37.500 0.00 0.00 41.95 2.71
3483 3594 5.885912 TGGGATAAAGAGTTGGCTTACAATC 59.114 40.000 0.00 0.00 41.95 2.67
3484 3595 5.007724 GGGATAAAGAGTTGGCTTACAATCG 59.992 44.000 0.00 0.00 41.95 3.34
3485 3596 3.831715 AAAGAGTTGGCTTACAATCGC 57.168 42.857 0.00 0.00 41.95 4.58
3486 3597 1.739067 AGAGTTGGCTTACAATCGCC 58.261 50.000 0.00 0.00 46.46 5.54
3492 3603 1.448985 GGCTTACAATCGCCACTTCA 58.551 50.000 0.00 0.00 45.59 3.02
3493 3604 1.130561 GGCTTACAATCGCCACTTCAC 59.869 52.381 0.00 0.00 45.59 3.18
3494 3605 1.804151 GCTTACAATCGCCACTTCACA 59.196 47.619 0.00 0.00 0.00 3.58
3495 3606 2.412847 GCTTACAATCGCCACTTCACAC 60.413 50.000 0.00 0.00 0.00 3.82
3496 3607 2.535012 TACAATCGCCACTTCACACA 57.465 45.000 0.00 0.00 0.00 3.72
3497 3608 1.674359 ACAATCGCCACTTCACACAA 58.326 45.000 0.00 0.00 0.00 3.33
3498 3609 2.229792 ACAATCGCCACTTCACACAAT 58.770 42.857 0.00 0.00 0.00 2.71
3499 3610 3.407698 ACAATCGCCACTTCACACAATA 58.592 40.909 0.00 0.00 0.00 1.90
3500 3611 3.188460 ACAATCGCCACTTCACACAATAC 59.812 43.478 0.00 0.00 0.00 1.89
3501 3612 2.535012 TCGCCACTTCACACAATACA 57.465 45.000 0.00 0.00 0.00 2.29
3502 3613 3.052455 TCGCCACTTCACACAATACAT 57.948 42.857 0.00 0.00 0.00 2.29
3503 3614 4.195225 TCGCCACTTCACACAATACATA 57.805 40.909 0.00 0.00 0.00 2.29
3504 3615 4.570930 TCGCCACTTCACACAATACATAA 58.429 39.130 0.00 0.00 0.00 1.90
3505 3616 4.998033 TCGCCACTTCACACAATACATAAA 59.002 37.500 0.00 0.00 0.00 1.40
3506 3617 5.645929 TCGCCACTTCACACAATACATAAAT 59.354 36.000 0.00 0.00 0.00 1.40
3507 3618 6.819146 TCGCCACTTCACACAATACATAAATA 59.181 34.615 0.00 0.00 0.00 1.40
3508 3619 7.497579 TCGCCACTTCACACAATACATAAATAT 59.502 33.333 0.00 0.00 0.00 1.28
3509 3620 8.769891 CGCCACTTCACACAATACATAAATATA 58.230 33.333 0.00 0.00 0.00 0.86
3536 3647 8.572855 TTCATACATCATCCAAAATACACACA 57.427 30.769 0.00 0.00 0.00 3.72
3537 3648 8.750515 TCATACATCATCCAAAATACACACAT 57.249 30.769 0.00 0.00 0.00 3.21
3538 3649 9.844257 TCATACATCATCCAAAATACACACATA 57.156 29.630 0.00 0.00 0.00 2.29
3544 3655 8.902540 TCATCCAAAATACACACATATAGACC 57.097 34.615 0.00 0.00 0.00 3.85
3545 3656 7.655732 TCATCCAAAATACACACATATAGACCG 59.344 37.037 0.00 0.00 0.00 4.79
3546 3657 7.114866 TCCAAAATACACACATATAGACCGA 57.885 36.000 0.00 0.00 0.00 4.69
3547 3658 6.982141 TCCAAAATACACACATATAGACCGAC 59.018 38.462 0.00 0.00 0.00 4.79
3548 3659 6.984474 CCAAAATACACACATATAGACCGACT 59.016 38.462 0.00 0.00 0.00 4.18
3549 3660 8.139350 CCAAAATACACACATATAGACCGACTA 58.861 37.037 0.00 0.00 35.42 2.59
3550 3661 8.965172 CAAAATACACACATATAGACCGACTAC 58.035 37.037 0.00 0.00 33.62 2.73
3551 3662 4.808077 ACACACATATAGACCGACTACG 57.192 45.455 0.00 0.00 39.43 3.51
3564 3675 3.226346 CGACTACGGTCAAAATCCAGA 57.774 47.619 0.00 0.00 42.21 3.86
3565 3676 3.782046 CGACTACGGTCAAAATCCAGAT 58.218 45.455 0.00 0.00 42.21 2.90
3566 3677 3.551890 CGACTACGGTCAAAATCCAGATG 59.448 47.826 0.00 0.00 42.21 2.90
3567 3678 4.676986 CGACTACGGTCAAAATCCAGATGA 60.677 45.833 0.00 0.00 42.21 2.92
3568 3679 5.160607 ACTACGGTCAAAATCCAGATGAA 57.839 39.130 0.00 0.00 0.00 2.57
3569 3680 5.556915 ACTACGGTCAAAATCCAGATGAAA 58.443 37.500 0.00 0.00 0.00 2.69
3570 3681 6.001460 ACTACGGTCAAAATCCAGATGAAAA 58.999 36.000 0.00 0.00 0.00 2.29
3571 3682 5.982890 ACGGTCAAAATCCAGATGAAAAT 57.017 34.783 0.00 0.00 0.00 1.82
3572 3683 7.827236 ACTACGGTCAAAATCCAGATGAAAATA 59.173 33.333 0.00 0.00 0.00 1.40
3573 3684 7.461182 ACGGTCAAAATCCAGATGAAAATAA 57.539 32.000 0.00 0.00 0.00 1.40
3574 3685 7.538575 ACGGTCAAAATCCAGATGAAAATAAG 58.461 34.615 0.00 0.00 0.00 1.73
3575 3686 7.393234 ACGGTCAAAATCCAGATGAAAATAAGA 59.607 33.333 0.00 0.00 0.00 2.10
3576 3687 7.698130 CGGTCAAAATCCAGATGAAAATAAGAC 59.302 37.037 0.00 0.00 0.00 3.01
3577 3688 8.522830 GGTCAAAATCCAGATGAAAATAAGACA 58.477 33.333 0.00 0.00 0.00 3.41
3578 3689 9.912634 GTCAAAATCCAGATGAAAATAAGACAA 57.087 29.630 0.00 0.00 0.00 3.18
3579 3690 9.912634 TCAAAATCCAGATGAAAATAAGACAAC 57.087 29.630 0.00 0.00 0.00 3.32
3580 3691 9.143631 CAAAATCCAGATGAAAATAAGACAACC 57.856 33.333 0.00 0.00 0.00 3.77
3581 3692 7.410120 AATCCAGATGAAAATAAGACAACCC 57.590 36.000 0.00 0.00 0.00 4.11
3582 3693 5.261216 TCCAGATGAAAATAAGACAACCCC 58.739 41.667 0.00 0.00 0.00 4.95
3583 3694 5.016173 CCAGATGAAAATAAGACAACCCCA 58.984 41.667 0.00 0.00 0.00 4.96
3584 3695 5.480073 CCAGATGAAAATAAGACAACCCCAA 59.520 40.000 0.00 0.00 0.00 4.12
3585 3696 6.014669 CCAGATGAAAATAAGACAACCCCAAA 60.015 38.462 0.00 0.00 0.00 3.28
3586 3697 7.310609 CCAGATGAAAATAAGACAACCCCAAAT 60.311 37.037 0.00 0.00 0.00 2.32
3587 3698 7.546667 CAGATGAAAATAAGACAACCCCAAATG 59.453 37.037 0.00 0.00 0.00 2.32
3588 3699 5.546526 TGAAAATAAGACAACCCCAAATGC 58.453 37.500 0.00 0.00 0.00 3.56
3589 3700 5.306678 TGAAAATAAGACAACCCCAAATGCT 59.693 36.000 0.00 0.00 0.00 3.79
3590 3701 6.495181 TGAAAATAAGACAACCCCAAATGCTA 59.505 34.615 0.00 0.00 0.00 3.49
3591 3702 6.530019 AAATAAGACAACCCCAAATGCTAG 57.470 37.500 0.00 0.00 0.00 3.42
3592 3703 3.806949 AAGACAACCCCAAATGCTAGA 57.193 42.857 0.00 0.00 0.00 2.43
3593 3704 4.322057 AAGACAACCCCAAATGCTAGAT 57.678 40.909 0.00 0.00 0.00 1.98
3594 3705 3.891049 AGACAACCCCAAATGCTAGATC 58.109 45.455 0.00 0.00 0.00 2.75
3595 3706 2.952310 GACAACCCCAAATGCTAGATCC 59.048 50.000 0.00 0.00 0.00 3.36
3596 3707 2.310538 CAACCCCAAATGCTAGATCCC 58.689 52.381 0.00 0.00 0.00 3.85
3597 3708 0.853530 ACCCCAAATGCTAGATCCCC 59.146 55.000 0.00 0.00 0.00 4.81
3598 3709 0.250901 CCCCAAATGCTAGATCCCCG 60.251 60.000 0.00 0.00 0.00 5.73
3599 3710 0.764890 CCCAAATGCTAGATCCCCGA 59.235 55.000 0.00 0.00 0.00 5.14
3600 3711 1.352352 CCCAAATGCTAGATCCCCGAT 59.648 52.381 0.00 0.00 0.00 4.18
3601 3712 2.616510 CCCAAATGCTAGATCCCCGATC 60.617 54.545 0.00 0.00 39.17 3.69
3602 3713 2.341257 CAAATGCTAGATCCCCGATCG 58.659 52.381 8.51 8.51 43.17 3.69
3603 3714 1.633774 AATGCTAGATCCCCGATCGT 58.366 50.000 15.09 0.00 43.17 3.73
3604 3715 1.178276 ATGCTAGATCCCCGATCGTC 58.822 55.000 15.09 4.78 43.17 4.20
3605 3716 0.894184 TGCTAGATCCCCGATCGTCC 60.894 60.000 15.09 0.00 43.17 4.79
3606 3717 1.596895 GCTAGATCCCCGATCGTCCC 61.597 65.000 15.09 0.00 43.17 4.46
3607 3718 0.251209 CTAGATCCCCGATCGTCCCA 60.251 60.000 15.09 0.00 43.17 4.37
3608 3719 0.186630 TAGATCCCCGATCGTCCCAA 59.813 55.000 15.09 0.00 43.17 4.12
3609 3720 1.069258 GATCCCCGATCGTCCCAAC 59.931 63.158 15.09 0.00 29.12 3.77
3610 3721 1.382695 ATCCCCGATCGTCCCAACT 60.383 57.895 15.09 0.00 0.00 3.16
3611 3722 1.686325 ATCCCCGATCGTCCCAACTG 61.686 60.000 15.09 0.00 0.00 3.16
3612 3723 2.186903 CCCGATCGTCCCAACTGG 59.813 66.667 15.09 1.09 0.00 4.00
3623 3734 2.377136 CCAACTGGGCTCCACTACT 58.623 57.895 0.00 0.00 0.00 2.57
3624 3735 0.036010 CCAACTGGGCTCCACTACTG 60.036 60.000 0.00 0.00 0.00 2.74
3625 3736 0.976641 CAACTGGGCTCCACTACTGA 59.023 55.000 0.00 0.00 0.00 3.41
3626 3737 1.556911 CAACTGGGCTCCACTACTGAT 59.443 52.381 0.00 0.00 0.00 2.90
3627 3738 1.490574 ACTGGGCTCCACTACTGATC 58.509 55.000 0.00 0.00 0.00 2.92
3628 3739 1.273267 ACTGGGCTCCACTACTGATCA 60.273 52.381 0.00 0.00 0.00 2.92
3629 3740 2.045524 CTGGGCTCCACTACTGATCAT 58.954 52.381 0.00 0.00 0.00 2.45
3630 3741 2.036992 CTGGGCTCCACTACTGATCATC 59.963 54.545 0.00 0.00 0.00 2.92
3631 3742 2.042464 GGGCTCCACTACTGATCATCA 58.958 52.381 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 8.621532 ACTATGAACATAACAGTTGACAACAT 57.378 30.769 20.08 8.51 0.00 2.71
175 176 0.171903 GACACCATGATGTTGCAGCC 59.828 55.000 0.00 0.00 31.24 4.85
295 297 7.207383 ACACATGAAATTCCATTGATATGCAG 58.793 34.615 0.00 0.00 0.00 4.41
365 367 6.957631 TCCACTCATTACCAGTGAATGTAAT 58.042 36.000 1.31 0.00 43.54 1.89
459 461 1.154854 CGCACACATGTCAACGACG 60.155 57.895 0.00 0.00 34.95 5.12
561 563 6.653320 GTGTAAGACTGAAACCATGGTATTCA 59.347 38.462 26.74 26.74 0.00 2.57
612 614 1.134128 AGACACCTGTGTTGTGCATCA 60.134 47.619 4.16 0.00 45.05 3.07
641 644 8.853077 TGAGTGTTGATAAATCTCAATCTTGT 57.147 30.769 12.93 0.00 37.47 3.16
673 676 5.420421 AGACTACTAGAGACAACACATGCAT 59.580 40.000 0.00 0.00 0.00 3.96
692 695 8.023021 ACATGCAATTGTAGATAGGAAGACTA 57.977 34.615 7.40 0.00 35.80 2.59
742 746 8.950210 TGAAGTTGACCTCAAGATTTTATCATC 58.050 33.333 0.00 0.00 36.39 2.92
781 785 5.826737 ACTGCTTATGAATCTCATTGGAAGG 59.173 40.000 0.00 0.00 38.26 3.46
1442 1447 2.808919 TCCTTCGTCTCTGTGATCCTT 58.191 47.619 0.00 0.00 0.00 3.36
1451 1456 1.270907 ATGGTGCTTCCTTCGTCTCT 58.729 50.000 0.80 0.00 37.07 3.10
1531 1536 2.672996 CTTGGCGTGGGGGAACAG 60.673 66.667 0.00 0.00 0.00 3.16
1567 1572 5.283060 AGACATTGATTACTTGTGTTCGC 57.717 39.130 0.00 0.00 0.00 4.70
1655 1660 9.056005 TCTCACATATATTAAATCTGCACAACC 57.944 33.333 0.00 0.00 0.00 3.77
1820 1884 4.314522 TGCCATATTGGAGTTTTCTGGA 57.685 40.909 0.00 0.00 40.96 3.86
1969 2033 8.853077 TTACGGTACTACATAGTATGTATGCT 57.147 34.615 20.65 10.60 44.11 3.79
1991 2055 9.289303 CACACATGCTTATTTTAGTGGAATTAC 57.711 33.333 0.00 0.00 0.00 1.89
1995 2059 6.892658 ACACACATGCTTATTTTAGTGGAA 57.107 33.333 0.00 0.00 0.00 3.53
2145 2249 9.410556 CCTACAAAAACAAGGTTCATTAGAATG 57.589 33.333 0.00 0.00 35.92 2.67
2236 2340 6.231211 ACTTGGACATGAGTTTTAGTAGTGG 58.769 40.000 0.00 0.00 0.00 4.00
2396 2500 1.207329 AGACCGGTAGAACCAAGCATC 59.793 52.381 7.34 0.00 38.47 3.91
2450 2554 6.098838 TGTTCATGACTATGGATGAGCTTACT 59.901 38.462 0.00 0.00 34.97 2.24
2451 2555 6.283694 TGTTCATGACTATGGATGAGCTTAC 58.716 40.000 0.00 0.00 34.97 2.34
3156 3263 2.745281 GTGGCGGTGCTTTGACTATAAA 59.255 45.455 0.00 0.00 0.00 1.40
3288 3398 8.340618 ACAAAGGTAATACTACGAGACAACTA 57.659 34.615 0.00 0.00 0.00 2.24
3345 3456 0.532573 AGATATAGCCGCATCGTGGG 59.467 55.000 0.00 0.00 33.18 4.61
3346 3457 1.469940 GGAGATATAGCCGCATCGTGG 60.470 57.143 0.00 0.00 36.10 4.94
3347 3458 1.469940 GGGAGATATAGCCGCATCGTG 60.470 57.143 0.00 0.00 0.00 4.35
3348 3459 0.818296 GGGAGATATAGCCGCATCGT 59.182 55.000 0.00 0.00 0.00 3.73
3349 3460 0.817654 TGGGAGATATAGCCGCATCG 59.182 55.000 0.00 0.00 0.00 3.84
3350 3461 1.469940 CGTGGGAGATATAGCCGCATC 60.470 57.143 0.00 0.00 0.00 3.91
3351 3462 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
3352 3463 0.826256 ACGTGGGAGATATAGCCGCA 60.826 55.000 0.00 0.00 0.00 5.69
3353 3464 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
3354 3465 0.959553 ACACGTGGGAGATATAGCCG 59.040 55.000 21.57 0.00 0.00 5.52
3355 3466 1.068472 CGACACGTGGGAGATATAGCC 60.068 57.143 21.57 0.00 0.00 3.93
3356 3467 1.878088 TCGACACGTGGGAGATATAGC 59.122 52.381 21.57 0.00 0.00 2.97
3357 3468 2.484651 CCTCGACACGTGGGAGATATAG 59.515 54.545 29.41 15.13 36.95 1.31
3358 3469 2.501261 CCTCGACACGTGGGAGATATA 58.499 52.381 29.41 5.30 36.95 0.86
3359 3470 1.319541 CCTCGACACGTGGGAGATAT 58.680 55.000 29.41 6.39 36.95 1.63
3360 3471 1.381928 GCCTCGACACGTGGGAGATA 61.382 60.000 29.41 7.54 40.31 1.98
3361 3472 2.711922 GCCTCGACACGTGGGAGAT 61.712 63.158 29.41 7.79 40.31 2.75
3362 3473 3.371063 GCCTCGACACGTGGGAGA 61.371 66.667 29.41 19.95 40.31 3.71
3363 3474 3.680786 TGCCTCGACACGTGGGAG 61.681 66.667 24.04 24.04 40.31 4.30
3364 3475 3.986006 GTGCCTCGACACGTGGGA 61.986 66.667 21.57 15.34 40.31 4.37
3373 3484 1.654954 GCCTCTAAGTCGTGCCTCGA 61.655 60.000 0.00 0.00 46.83 4.04
3374 3485 1.226717 GCCTCTAAGTCGTGCCTCG 60.227 63.158 0.00 0.00 41.41 4.63
3375 3486 0.461961 ATGCCTCTAAGTCGTGCCTC 59.538 55.000 0.00 0.00 0.00 4.70
3376 3487 1.776662 TATGCCTCTAAGTCGTGCCT 58.223 50.000 0.00 0.00 0.00 4.75
3377 3488 2.202566 GTTATGCCTCTAAGTCGTGCC 58.797 52.381 0.00 0.00 0.00 5.01
3378 3489 2.202566 GGTTATGCCTCTAAGTCGTGC 58.797 52.381 0.00 0.00 0.00 5.34
3379 3490 2.460918 CGGTTATGCCTCTAAGTCGTG 58.539 52.381 0.00 0.00 34.25 4.35
3380 3491 1.202382 GCGGTTATGCCTCTAAGTCGT 60.202 52.381 0.00 0.00 34.25 4.34
3381 3492 1.202371 TGCGGTTATGCCTCTAAGTCG 60.202 52.381 0.00 0.00 34.25 4.18
3382 3493 2.596904 TGCGGTTATGCCTCTAAGTC 57.403 50.000 0.00 0.00 34.25 3.01
3383 3494 3.641906 ACTATGCGGTTATGCCTCTAAGT 59.358 43.478 0.00 0.00 34.25 2.24
3384 3495 3.990469 CACTATGCGGTTATGCCTCTAAG 59.010 47.826 0.00 0.00 34.25 2.18
3385 3496 3.244078 CCACTATGCGGTTATGCCTCTAA 60.244 47.826 0.00 0.00 34.25 2.10
3386 3497 2.299013 CCACTATGCGGTTATGCCTCTA 59.701 50.000 0.00 0.00 34.25 2.43
3387 3498 1.070758 CCACTATGCGGTTATGCCTCT 59.929 52.381 0.00 0.00 34.25 3.69
3388 3499 1.202651 ACCACTATGCGGTTATGCCTC 60.203 52.381 0.00 0.00 30.53 4.70
3389 3500 0.837272 ACCACTATGCGGTTATGCCT 59.163 50.000 0.00 0.00 30.53 4.75
3390 3501 1.675552 AACCACTATGCGGTTATGCC 58.324 50.000 0.00 0.00 45.00 4.40
3391 3502 3.119637 ACAAAACCACTATGCGGTTATGC 60.120 43.478 0.00 0.00 46.12 3.14
3392 3503 4.658071 GACAAAACCACTATGCGGTTATG 58.342 43.478 0.00 0.00 46.12 1.90
3393 3504 3.372822 CGACAAAACCACTATGCGGTTAT 59.627 43.478 0.00 0.00 46.12 1.89
3394 3505 2.737783 CGACAAAACCACTATGCGGTTA 59.262 45.455 0.00 0.00 46.12 2.85
3396 3507 1.153353 CGACAAAACCACTATGCGGT 58.847 50.000 0.00 0.00 38.85 5.68
3397 3508 0.179200 GCGACAAAACCACTATGCGG 60.179 55.000 0.00 0.00 0.00 5.69
3398 3509 0.515127 TGCGACAAAACCACTATGCG 59.485 50.000 0.00 0.00 0.00 4.73
3399 3510 2.225491 TCTTGCGACAAAACCACTATGC 59.775 45.455 0.00 0.00 0.00 3.14
3400 3511 4.466828 CTTCTTGCGACAAAACCACTATG 58.533 43.478 0.00 0.00 0.00 2.23
3401 3512 3.502211 CCTTCTTGCGACAAAACCACTAT 59.498 43.478 0.00 0.00 0.00 2.12
3402 3513 2.875933 CCTTCTTGCGACAAAACCACTA 59.124 45.455 0.00 0.00 0.00 2.74
3403 3514 1.676006 CCTTCTTGCGACAAAACCACT 59.324 47.619 0.00 0.00 0.00 4.00
3404 3515 1.269051 CCCTTCTTGCGACAAAACCAC 60.269 52.381 0.00 0.00 0.00 4.16
3405 3516 1.028905 CCCTTCTTGCGACAAAACCA 58.971 50.000 0.00 0.00 0.00 3.67
3406 3517 1.001706 GACCCTTCTTGCGACAAAACC 60.002 52.381 0.00 0.00 0.00 3.27
3407 3518 1.673920 TGACCCTTCTTGCGACAAAAC 59.326 47.619 0.00 0.00 0.00 2.43
3408 3519 2.045561 TGACCCTTCTTGCGACAAAA 57.954 45.000 0.00 0.00 0.00 2.44
3409 3520 2.151202 GATGACCCTTCTTGCGACAAA 58.849 47.619 0.00 0.00 0.00 2.83
3410 3521 1.347707 AGATGACCCTTCTTGCGACAA 59.652 47.619 0.00 0.00 0.00 3.18
3411 3522 0.976641 AGATGACCCTTCTTGCGACA 59.023 50.000 0.00 0.00 0.00 4.35
3412 3523 2.003301 GAAGATGACCCTTCTTGCGAC 58.997 52.381 0.00 0.00 39.44 5.19
3413 3524 1.623311 TGAAGATGACCCTTCTTGCGA 59.377 47.619 0.00 0.00 42.20 5.10
3414 3525 1.734465 GTGAAGATGACCCTTCTTGCG 59.266 52.381 0.00 0.00 42.20 4.85
3415 3526 2.485814 GTGTGAAGATGACCCTTCTTGC 59.514 50.000 0.00 0.00 42.20 4.01
3416 3527 3.743521 TGTGTGAAGATGACCCTTCTTG 58.256 45.455 0.00 0.00 42.20 3.02
3417 3528 4.437682 TTGTGTGAAGATGACCCTTCTT 57.562 40.909 0.00 0.00 42.20 2.52
3418 3529 4.566488 GGATTGTGTGAAGATGACCCTTCT 60.566 45.833 0.00 0.00 42.20 2.85
3419 3530 3.691609 GGATTGTGTGAAGATGACCCTTC 59.308 47.826 0.00 0.00 42.09 3.46
3420 3531 3.562176 GGGATTGTGTGAAGATGACCCTT 60.562 47.826 0.00 0.00 32.93 3.95
3421 3532 2.025887 GGGATTGTGTGAAGATGACCCT 60.026 50.000 0.00 0.00 32.93 4.34
3422 3533 2.290896 TGGGATTGTGTGAAGATGACCC 60.291 50.000 0.00 0.00 35.82 4.46
3423 3534 3.071874 TGGGATTGTGTGAAGATGACC 57.928 47.619 0.00 0.00 0.00 4.02
3424 3535 4.012374 ACATGGGATTGTGTGAAGATGAC 58.988 43.478 0.00 0.00 0.00 3.06
3425 3536 4.305539 ACATGGGATTGTGTGAAGATGA 57.694 40.909 0.00 0.00 0.00 2.92
3426 3537 6.319405 TCATTACATGGGATTGTGTGAAGATG 59.681 38.462 0.00 0.00 0.00 2.90
3427 3538 6.425735 TCATTACATGGGATTGTGTGAAGAT 58.574 36.000 0.00 0.00 0.00 2.40
3428 3539 5.814481 TCATTACATGGGATTGTGTGAAGA 58.186 37.500 0.00 0.00 0.00 2.87
3429 3540 6.072008 TGTTCATTACATGGGATTGTGTGAAG 60.072 38.462 0.00 0.00 36.80 3.02
3430 3541 5.772169 TGTTCATTACATGGGATTGTGTGAA 59.228 36.000 0.00 0.00 35.28 3.18
3431 3542 5.320277 TGTTCATTACATGGGATTGTGTGA 58.680 37.500 0.00 0.00 0.00 3.58
3432 3543 5.641783 TGTTCATTACATGGGATTGTGTG 57.358 39.130 0.00 0.00 0.00 3.82
3433 3544 6.009589 TCTTGTTCATTACATGGGATTGTGT 58.990 36.000 0.00 0.00 36.44 3.72
3434 3545 6.513806 TCTTGTTCATTACATGGGATTGTG 57.486 37.500 0.00 0.00 36.44 3.33
3435 3546 7.364056 CCATTCTTGTTCATTACATGGGATTGT 60.364 37.037 0.00 0.00 36.44 2.71
3436 3547 6.982141 CCATTCTTGTTCATTACATGGGATTG 59.018 38.462 0.00 0.00 36.44 2.67
3437 3548 7.116075 CCATTCTTGTTCATTACATGGGATT 57.884 36.000 0.00 0.00 36.44 3.01
3438 3549 6.720112 CCATTCTTGTTCATTACATGGGAT 57.280 37.500 0.00 0.00 36.44 3.85
3440 3551 5.266733 CCCATTCTTGTTCATTACATGGG 57.733 43.478 0.00 0.00 43.44 4.00
3441 3552 6.720112 ATCCCATTCTTGTTCATTACATGG 57.280 37.500 0.00 0.00 36.44 3.66
3442 3553 9.740239 CTTTATCCCATTCTTGTTCATTACATG 57.260 33.333 0.00 0.00 36.44 3.21
3443 3554 9.699410 TCTTTATCCCATTCTTGTTCATTACAT 57.301 29.630 0.00 0.00 36.44 2.29
3444 3555 9.177608 CTCTTTATCCCATTCTTGTTCATTACA 57.822 33.333 0.00 0.00 34.12 2.41
3445 3556 9.178758 ACTCTTTATCCCATTCTTGTTCATTAC 57.821 33.333 0.00 0.00 0.00 1.89
3446 3557 9.753674 AACTCTTTATCCCATTCTTGTTCATTA 57.246 29.630 0.00 0.00 0.00 1.90
3447 3558 8.526147 CAACTCTTTATCCCATTCTTGTTCATT 58.474 33.333 0.00 0.00 0.00 2.57
3448 3559 7.123247 CCAACTCTTTATCCCATTCTTGTTCAT 59.877 37.037 0.00 0.00 0.00 2.57
3449 3560 6.434028 CCAACTCTTTATCCCATTCTTGTTCA 59.566 38.462 0.00 0.00 0.00 3.18
3450 3561 6.625960 GCCAACTCTTTATCCCATTCTTGTTC 60.626 42.308 0.00 0.00 0.00 3.18
3451 3562 5.185828 GCCAACTCTTTATCCCATTCTTGTT 59.814 40.000 0.00 0.00 0.00 2.83
3452 3563 4.706962 GCCAACTCTTTATCCCATTCTTGT 59.293 41.667 0.00 0.00 0.00 3.16
3453 3564 4.952335 AGCCAACTCTTTATCCCATTCTTG 59.048 41.667 0.00 0.00 0.00 3.02
3454 3565 5.198602 AGCCAACTCTTTATCCCATTCTT 57.801 39.130 0.00 0.00 0.00 2.52
3455 3566 4.870021 AGCCAACTCTTTATCCCATTCT 57.130 40.909 0.00 0.00 0.00 2.40
3456 3567 5.885912 TGTAAGCCAACTCTTTATCCCATTC 59.114 40.000 0.00 0.00 0.00 2.67
3457 3568 5.826643 TGTAAGCCAACTCTTTATCCCATT 58.173 37.500 0.00 0.00 0.00 3.16
3458 3569 5.450818 TGTAAGCCAACTCTTTATCCCAT 57.549 39.130 0.00 0.00 0.00 4.00
3459 3570 4.919774 TGTAAGCCAACTCTTTATCCCA 57.080 40.909 0.00 0.00 0.00 4.37
3460 3571 5.007724 CGATTGTAAGCCAACTCTTTATCCC 59.992 44.000 0.00 0.00 35.44 3.85
3461 3572 5.504173 GCGATTGTAAGCCAACTCTTTATCC 60.504 44.000 0.00 0.00 35.44 2.59
3462 3573 5.502606 GCGATTGTAAGCCAACTCTTTATC 58.497 41.667 0.00 0.00 35.44 1.75
3463 3574 5.485662 GCGATTGTAAGCCAACTCTTTAT 57.514 39.130 0.00 0.00 35.44 1.40
3464 3575 4.939509 GCGATTGTAAGCCAACTCTTTA 57.060 40.909 0.00 0.00 35.44 1.85
3465 3576 3.831715 GCGATTGTAAGCCAACTCTTT 57.168 42.857 0.00 0.00 35.44 2.52
3474 3585 1.804151 TGTGAAGTGGCGATTGTAAGC 59.196 47.619 0.00 0.00 0.00 3.09
3475 3586 2.805671 TGTGTGAAGTGGCGATTGTAAG 59.194 45.455 0.00 0.00 0.00 2.34
3476 3587 2.839975 TGTGTGAAGTGGCGATTGTAA 58.160 42.857 0.00 0.00 0.00 2.41
3477 3588 2.535012 TGTGTGAAGTGGCGATTGTA 57.465 45.000 0.00 0.00 0.00 2.41
3478 3589 1.674359 TTGTGTGAAGTGGCGATTGT 58.326 45.000 0.00 0.00 0.00 2.71
3479 3590 2.995466 ATTGTGTGAAGTGGCGATTG 57.005 45.000 0.00 0.00 0.00 2.67
3480 3591 3.407698 TGTATTGTGTGAAGTGGCGATT 58.592 40.909 0.00 0.00 0.00 3.34
3481 3592 3.052455 TGTATTGTGTGAAGTGGCGAT 57.948 42.857 0.00 0.00 0.00 4.58
3482 3593 2.535012 TGTATTGTGTGAAGTGGCGA 57.465 45.000 0.00 0.00 0.00 5.54
3483 3594 4.937696 TTATGTATTGTGTGAAGTGGCG 57.062 40.909 0.00 0.00 0.00 5.69
3510 3621 9.187996 TGTGTGTATTTTGGATGATGTATGAAT 57.812 29.630 0.00 0.00 0.00 2.57
3511 3622 8.572855 TGTGTGTATTTTGGATGATGTATGAA 57.427 30.769 0.00 0.00 0.00 2.57
3512 3623 8.750515 ATGTGTGTATTTTGGATGATGTATGA 57.249 30.769 0.00 0.00 0.00 2.15
3518 3629 9.507329 GGTCTATATGTGTGTATTTTGGATGAT 57.493 33.333 0.00 0.00 0.00 2.45
3519 3630 7.655732 CGGTCTATATGTGTGTATTTTGGATGA 59.344 37.037 0.00 0.00 0.00 2.92
3520 3631 7.655732 TCGGTCTATATGTGTGTATTTTGGATG 59.344 37.037 0.00 0.00 0.00 3.51
3521 3632 7.656137 GTCGGTCTATATGTGTGTATTTTGGAT 59.344 37.037 0.00 0.00 0.00 3.41
3522 3633 6.982141 GTCGGTCTATATGTGTGTATTTTGGA 59.018 38.462 0.00 0.00 0.00 3.53
3523 3634 6.984474 AGTCGGTCTATATGTGTGTATTTTGG 59.016 38.462 0.00 0.00 0.00 3.28
3524 3635 8.965172 GTAGTCGGTCTATATGTGTGTATTTTG 58.035 37.037 0.00 0.00 0.00 2.44
3525 3636 7.859377 CGTAGTCGGTCTATATGTGTGTATTTT 59.141 37.037 0.00 0.00 0.00 1.82
3526 3637 7.358066 CGTAGTCGGTCTATATGTGTGTATTT 58.642 38.462 0.00 0.00 0.00 1.40
3527 3638 6.895898 CGTAGTCGGTCTATATGTGTGTATT 58.104 40.000 0.00 0.00 0.00 1.89
3528 3639 6.477669 CGTAGTCGGTCTATATGTGTGTAT 57.522 41.667 0.00 0.00 0.00 2.29
3529 3640 5.912360 CGTAGTCGGTCTATATGTGTGTA 57.088 43.478 0.00 0.00 0.00 2.90
3530 3641 4.808077 CGTAGTCGGTCTATATGTGTGT 57.192 45.455 0.00 0.00 0.00 3.72
3544 3655 3.226346 TCTGGATTTTGACCGTAGTCG 57.774 47.619 0.00 0.00 46.74 4.18
3545 3656 4.755411 TCATCTGGATTTTGACCGTAGTC 58.245 43.478 0.00 0.00 43.83 2.59
3546 3657 4.819105 TCATCTGGATTTTGACCGTAGT 57.181 40.909 0.00 0.00 0.00 2.73
3547 3658 6.494893 TTTTCATCTGGATTTTGACCGTAG 57.505 37.500 0.00 0.00 0.00 3.51
3548 3659 8.568676 TTATTTTCATCTGGATTTTGACCGTA 57.431 30.769 0.00 0.00 0.00 4.02
3549 3660 5.982890 ATTTTCATCTGGATTTTGACCGT 57.017 34.783 0.00 0.00 0.00 4.83
3550 3661 7.698130 GTCTTATTTTCATCTGGATTTTGACCG 59.302 37.037 0.00 0.00 0.00 4.79
3551 3662 8.522830 TGTCTTATTTTCATCTGGATTTTGACC 58.477 33.333 0.00 0.00 0.00 4.02
3552 3663 9.912634 TTGTCTTATTTTCATCTGGATTTTGAC 57.087 29.630 0.00 0.00 0.00 3.18
3553 3664 9.912634 GTTGTCTTATTTTCATCTGGATTTTGA 57.087 29.630 0.00 0.00 0.00 2.69
3554 3665 9.143631 GGTTGTCTTATTTTCATCTGGATTTTG 57.856 33.333 0.00 0.00 0.00 2.44
3555 3666 8.314021 GGGTTGTCTTATTTTCATCTGGATTTT 58.686 33.333 0.00 0.00 0.00 1.82
3556 3667 7.093333 GGGGTTGTCTTATTTTCATCTGGATTT 60.093 37.037 0.00 0.00 0.00 2.17
3557 3668 6.381133 GGGGTTGTCTTATTTTCATCTGGATT 59.619 38.462 0.00 0.00 0.00 3.01
3558 3669 5.893824 GGGGTTGTCTTATTTTCATCTGGAT 59.106 40.000 0.00 0.00 0.00 3.41
3559 3670 5.222233 TGGGGTTGTCTTATTTTCATCTGGA 60.222 40.000 0.00 0.00 0.00 3.86
3560 3671 5.016173 TGGGGTTGTCTTATTTTCATCTGG 58.984 41.667 0.00 0.00 0.00 3.86
3561 3672 6.588719 TTGGGGTTGTCTTATTTTCATCTG 57.411 37.500 0.00 0.00 0.00 2.90
3562 3673 7.614494 CATTTGGGGTTGTCTTATTTTCATCT 58.386 34.615 0.00 0.00 0.00 2.90
3563 3674 6.313658 GCATTTGGGGTTGTCTTATTTTCATC 59.686 38.462 0.00 0.00 0.00 2.92
3564 3675 6.013466 AGCATTTGGGGTTGTCTTATTTTCAT 60.013 34.615 0.00 0.00 0.00 2.57
3565 3676 5.306678 AGCATTTGGGGTTGTCTTATTTTCA 59.693 36.000 0.00 0.00 0.00 2.69
3566 3677 5.793817 AGCATTTGGGGTTGTCTTATTTTC 58.206 37.500 0.00 0.00 0.00 2.29
3567 3678 5.823861 AGCATTTGGGGTTGTCTTATTTT 57.176 34.783 0.00 0.00 0.00 1.82
3568 3679 6.252995 TCTAGCATTTGGGGTTGTCTTATTT 58.747 36.000 0.00 0.00 0.00 1.40
3569 3680 5.826643 TCTAGCATTTGGGGTTGTCTTATT 58.173 37.500 0.00 0.00 0.00 1.40
3570 3681 5.450818 TCTAGCATTTGGGGTTGTCTTAT 57.549 39.130 0.00 0.00 0.00 1.73
3571 3682 4.919774 TCTAGCATTTGGGGTTGTCTTA 57.080 40.909 0.00 0.00 0.00 2.10
3572 3683 3.806949 TCTAGCATTTGGGGTTGTCTT 57.193 42.857 0.00 0.00 0.00 3.01
3573 3684 3.372025 GGATCTAGCATTTGGGGTTGTCT 60.372 47.826 0.00 0.00 0.00 3.41
3574 3685 2.952310 GGATCTAGCATTTGGGGTTGTC 59.048 50.000 0.00 0.00 0.00 3.18
3575 3686 2.358195 GGGATCTAGCATTTGGGGTTGT 60.358 50.000 0.00 0.00 0.00 3.32
3576 3687 2.310538 GGGATCTAGCATTTGGGGTTG 58.689 52.381 0.00 0.00 0.00 3.77
3577 3688 1.217942 GGGGATCTAGCATTTGGGGTT 59.782 52.381 0.00 0.00 0.00 4.11
3578 3689 0.853530 GGGGATCTAGCATTTGGGGT 59.146 55.000 0.00 0.00 0.00 4.95
3579 3690 0.250901 CGGGGATCTAGCATTTGGGG 60.251 60.000 0.00 0.00 0.00 4.96
3580 3691 0.764890 TCGGGGATCTAGCATTTGGG 59.235 55.000 0.00 0.00 0.00 4.12
3581 3692 2.704572 GATCGGGGATCTAGCATTTGG 58.295 52.381 0.00 0.00 36.27 3.28
3582 3693 2.289072 ACGATCGGGGATCTAGCATTTG 60.289 50.000 20.98 0.00 36.96 2.32
3583 3694 1.971357 ACGATCGGGGATCTAGCATTT 59.029 47.619 20.98 0.00 36.96 2.32
3584 3695 1.546476 GACGATCGGGGATCTAGCATT 59.454 52.381 20.98 0.00 36.96 3.56
3585 3696 1.178276 GACGATCGGGGATCTAGCAT 58.822 55.000 20.98 0.00 36.96 3.79
3586 3697 0.894184 GGACGATCGGGGATCTAGCA 60.894 60.000 20.98 0.00 36.96 3.49
3587 3698 1.596895 GGGACGATCGGGGATCTAGC 61.597 65.000 20.98 0.00 36.96 3.42
3588 3699 0.251209 TGGGACGATCGGGGATCTAG 60.251 60.000 20.98 0.00 36.96 2.43
3589 3700 0.186630 TTGGGACGATCGGGGATCTA 59.813 55.000 20.98 0.00 36.96 1.98
3590 3701 1.075525 TTGGGACGATCGGGGATCT 60.076 57.895 20.98 0.00 36.96 2.75
3591 3702 1.069258 GTTGGGACGATCGGGGATC 59.931 63.158 20.98 7.51 35.88 3.36
3592 3703 1.382695 AGTTGGGACGATCGGGGAT 60.383 57.895 20.98 0.00 0.00 3.85
3593 3704 2.038329 AGTTGGGACGATCGGGGA 59.962 61.111 20.98 0.00 0.00 4.81
3594 3705 2.186903 CAGTTGGGACGATCGGGG 59.813 66.667 20.98 0.00 0.00 5.73
3595 3706 2.186903 CCAGTTGGGACGATCGGG 59.813 66.667 20.98 4.12 40.01 5.14
3605 3716 0.036010 CAGTAGTGGAGCCCAGTTGG 60.036 60.000 6.85 0.00 38.30 3.77
3606 3717 0.976641 TCAGTAGTGGAGCCCAGTTG 59.023 55.000 6.85 1.82 38.30 3.16
3607 3718 1.834263 GATCAGTAGTGGAGCCCAGTT 59.166 52.381 6.85 0.00 38.30 3.16
3608 3719 1.273267 TGATCAGTAGTGGAGCCCAGT 60.273 52.381 6.76 6.76 40.67 4.00
3609 3720 1.489481 TGATCAGTAGTGGAGCCCAG 58.511 55.000 0.00 0.00 32.34 4.45
3610 3721 2.042464 GATGATCAGTAGTGGAGCCCA 58.958 52.381 0.09 0.00 0.00 5.36
3611 3722 2.036992 CTGATGATCAGTAGTGGAGCCC 59.963 54.545 14.17 0.00 39.58 5.19
3612 3723 2.036992 CCTGATGATCAGTAGTGGAGCC 59.963 54.545 20.06 0.00 42.80 4.70
3613 3724 2.961741 TCCTGATGATCAGTAGTGGAGC 59.038 50.000 20.06 0.00 42.80 4.70
3614 3725 5.604758 TTTCCTGATGATCAGTAGTGGAG 57.395 43.478 20.06 4.25 42.80 3.86
3615 3726 5.721480 TCTTTTCCTGATGATCAGTAGTGGA 59.279 40.000 20.06 8.78 42.80 4.02
3616 3727 5.814705 GTCTTTTCCTGATGATCAGTAGTGG 59.185 44.000 20.06 6.52 42.80 4.00
3617 3728 6.312426 GTGTCTTTTCCTGATGATCAGTAGTG 59.688 42.308 20.06 5.96 42.80 2.74
3618 3729 6.014242 TGTGTCTTTTCCTGATGATCAGTAGT 60.014 38.462 20.06 0.00 42.80 2.73
3619 3730 6.401394 TGTGTCTTTTCCTGATGATCAGTAG 58.599 40.000 20.06 11.74 42.80 2.57
3620 3731 6.358974 TGTGTCTTTTCCTGATGATCAGTA 57.641 37.500 20.06 2.34 42.80 2.74
3621 3732 5.233083 TGTGTCTTTTCCTGATGATCAGT 57.767 39.130 20.06 0.00 42.80 3.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.